If you had the same issue I did, I suspect that your project builds but code-completion / code highlighting fails? I've just found some notes that may be useful. Here's what I did:
For language 'GNU C++' I added:
/usr/include
/usr/include/c++/4.6
/usr/include/c++/4.6/bits
/usr/include/i386-linux-gnu
/usr/include/i386-linux-gnu/bits
/usr/include/c++/4.6/debug
/usr/include/c++/4.6/i686-linux-gnu
/usr/include/c++/4.6/i686-linux-gnu/bits
For "GNU C" I added:
/usr/include
/usr/include/i386-linux-gnu
/usr/include/i386-linux-gnu/bits
TBH, I don't think all the directories above are actually required (you could probably remove the 'bits' directories) but the list above worked for me at the time.
I am now using Eclipse Indigo (version 3.7.2) from eclipse.org and it automatically finds and adds the correct include directories. The list is different for me:
/usr/include/c++/4.6
/usr/include/c++/4.6/i686-linux-gnu
/usr/include/c++/4.6/backward
/usr/lib/gcc/i686-linux-gnu/4.6/include
/usr/local/include
/usr/lib/gcc/i686-linux-gnu/4.6/include-fixed
/usr/include/i386-linux-gnu
/usr/include
Clearly, only add the include directories that actually exist on your system ;-)
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